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Installation

Autonima needs Python 3.10 or newer (tested on 3.10 through 3.13).

Full Install

git clone https://github.com/neurostuff/autonima.git
cd autonima
pip install -e ".[llm,meta,ui]"

This covers screening, parsing and annotation, autonima meta and autonima ui. Keep the quotes around the extras: unquoted brackets fail in zsh.

Before a real run, set OPENAI_API_KEY in your environment and put a contact address in the config's search.email, which NCBI asks for.

Base Install

pip install -e .

The base install gives you the package and CLI, with no LLM client: it can run autonima run-search but not screening.

Optional Extras

LLM Support

Install this for screening and other OpenAI-compatible model calls:

pip install -e ".[llm]"

Environment variables:

  • OPENAI_API_KEY for authentication
  • OPENAI_API_GATEWAY (optional) to override the OpenAI SDK gateway/base URL

Meta-Analysis Support

Install this to use autonima meta:

pip install -e ".[meta]"

This adds the NiMARE dependency stack. autonima meta needs NiMARE 0.11.0 or later.

Enhanced HTML Cleaning (Optional)

Install this for readabilipy-based HTML extraction:

pip install -e ".[readability]"

Notes:

  • readabilipy also requires Node.js on the system.
  • If it is not installed, Autonima falls back to basic HTML cleaning.

Documentation Tooling

Install this if you want to build the docs site locally:

pip install -e ".[docs]"

If you are actively working on the package and docs:

pip install -e ".[dev,llm,docs]"

Add meta and readability only if you need those workflows locally.